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chore: rerun after merge, with RAVEN functions
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@edkerk
edkerk committed May 9, 2022
1 parent 8be4ef3 commit 123eef9
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16 changes: 4 additions & 12 deletions code/modelCuration/addDBNewGeneAnnotation.m
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Expand Up @@ -20,31 +20,23 @@
fclose(fid);
for i = 1:length(newGPR.ID)
rxnIndex = find(strcmp(model.rxns, newGPR.ID(i)));
model = changeGeneAssociation(model, model.rxns{rxnIndex}, newGPR.GPR{i});
model = changeGrRules(model, model.rxns{rxnIndex}, newGPR.GPR{i});
end

% Delete unused genes (if any)
model = removeUnusedGenes(model);

model = deleteUnusedGenes(model);
% Add gene standard name for new genes
fid = fopen('../data/databases/SGDgeneNames.tsv');
yeast_gene_annotation = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
fclose(fid);
for i = 1: length(model.genes)
geneIndex = strcmp(yeast_gene_annotation{1}, model.genes{i});
if sum(geneIndex) == 1 && ~isempty(yeast_gene_annotation{2}{geneIndex})
model.geneNames{i} = yeast_gene_annotation{2}{geneIndex};
model.geneShortNames{i} = yeast_gene_annotation{2}{geneIndex};
else
model.geneNames{i} = model.genes{i};
model.geneShortNames{i} = model.genes{i};
end
end

% Add protein name for genes
for i = 1:length(model.genes)
model.proteins{i} = strcat('COBRAProtein',num2str(i));
end

% Save model:
model = rmfield(model,'grRules');
saveYeastModel(model)
cd modelCuration
62 changes: 31 additions & 31 deletions data/modelCuration/databasenewGPR.tsv
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@@ -1,29 +1,29 @@
rxnID_yeast_model genes_yeast_model final_GPR
r_0005 YGR032W or YMR306W or (YLR342W and YCR034W) ( YPR165W and YLR342W ) or ( YPR165W and YGR032W ) or ( YPR165W and YMR306W )
r_0005 YGR032W or YMR306W or (YLR342W and YCR034W) (YPR165W and YLR342W) or (YPR165W and YGR032W) or (YPR165W and YMR306W)
r_0021 YDR204W and YGL119W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C YDR204W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C
r_0022 YDR204W and YGL119W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C YDR204W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C
r_0263 ( YHL003C and YMR298W ) or ( YKL008C and YMR298W ) YKL008C and YHL003C and YMR298W
r_0264 ( YHL003C and YMR298W ) or ( YKL008C and YMR298W ) YKL008C and YHL003C and YMR298W
r_0265 ( YHL003C and YMR298W ) or ( YKL008C and YMR298W ) YKL008C and YHL003C and YMR298W
r_0266 ( YHL003C and YMR298W ) or ( YKL008C and YMR298W ) YKL008C and YHL003C and YMR298W
r_0263 (YHL003C and YMR298W) or (YKL008C and YMR298W) YKL008C and YHL003C and YMR298W
r_0264 (YHL003C and YMR298W) or (YKL008C and YMR298W) YKL008C and YHL003C and YMR298W
r_0265 (YHL003C and YMR298W) or (YKL008C and YMR298W) YKL008C and YHL003C and YMR298W
r_0266 (YHL003C and YMR298W) or (YKL008C and YMR298W) YKL008C and YHL003C and YMR298W
r_0532 YDR204W and YGL119W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C YDR204W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C
r_0831 YDR148C and YFL018C and YIL125W ( YDR148C and YFL018C and YIL125W and YFR049W ) or ( YDR148C and YFL018C and YIL125W )
r_0832 YDR148C and YFL018C and YIL125W ( YDR148C and YFL018C and YIL125W and YFR049W ) or ( YDR148C and YFL018C and YIL125W )
r_0852 YDR148C and YFL018C and YIL125W ( YFL022C and YLR060W )
r_0906 ( YKL088W and YKR072C and YOR054C ) or ( YKL088W and YKR072C ) or ( YKL088W and YOR054C ) or YKL088W YKL088W and YKR072C and YOR054C
r_0831 YDR148C and YFL018C and YIL125W (YDR148C and YFL018C and YIL125W and YFR049W) or (YDR148C and YFL018C and YIL125W)
r_0832 YDR148C and YFL018C and YIL125W (YDR148C and YFL018C and YIL125W and YFR049W) or (YDR148C and YFL018C and YIL125W)
r_0852 YDR148C and YFL018C and YIL125W (YFL022C and YLR060W)
r_0906 (YKL088W and YKR072C and YOR054C) or (YKL088W and YKR072C) or (YKL088W and YOR054C) or YKL088W YKL088W and YKR072C and YOR054C
r_0943 YDR400W and YLR017W and YLR209C YLR209C
r_0963 YDR204W and YGL119W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C YDR204W and YGR255C and YLR201C and YML110C and YOL096C and YOR126C
r_0985 YDR204W and YGL119W and YGR255C and YLR201C and YML110C and YOL096C and YOR125C YDR204W and YGR255C and YLR201C and YML110C and YOL096C and YOR126C
r_0992 ( YDL040C and YGR147C and YHR013C ) or ( YDL040C and YGR147C ) YHR013C and YDL040C and YOR253W
r_0993 ( YBR058C-A and YDR062W and YMR296C ) or ( YDR062W and YMR296C ) YMR296C and YKL212W and YDR062W and YGR038W and YLR350W and YBR058C-A
r_2852 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2853 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2854 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2855 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2856 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2857 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2858 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_2859 YBR097W and YLR240W ( YBR097W and YLR240W ) or ( YBR097W and YLR240W and YPL120W and YLR360W ) or ( YBR097W and YLR240W and YBR128C and YPL120W and YLR211C )
r_0992 (YDL040C and YGR147C and YHR013C) or (YDL040C and YGR147C) YHR013C and YDL040C and YOR253W
r_0993 (YBR058C-A and YDR062W and YMR296C) or (YDR062W and YMR296C) YMR296C and YKL212W and YDR062W and YGR038W and YLR350W and YBR058C-A
r_2852 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2853 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2854 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2855 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2856 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2857 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2858 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_2859 YBR097W and YLR240W (YBR097W and YLR240W) or (YBR097W and YLR240W and YPL120W and YLR360W) or (YBR097W and YLR240W and YBR128C and YPL120W and YLR211C)
r_3216 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
r_3217 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
r_3218 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
Expand All @@ -32,15 +32,15 @@ r_3220 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR38
r_3221 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
r_3222 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
r_3223 YLR386W and YNL325C YFR019W and YNL325C and YFR021W and YNL054W and YLR386W
r_1085 YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YMR054W and YOR332W and YPL234C and YPR036W ( YPR170W-B and YBR127C and YDL185W and YOR332W and YHR026W and YEL027W and YKL080W and YLR447C and YEL051W and YPL234C and YMR054W and YGR020C and YPR036W and YHR039C-A and YGR106C and YCL005W-A ) or ( YBR127C and YDL185W and YOR332W and YHR026W and YEL027W and YKL080W and YLR447C and YEL051W and YPL234C and YMR054W and YGR020C and YPR036W and YHR039C-A and YGR106C and YCL005W-A )
r_1086 YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W ( YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W and YPR170W-B and YGR106C and YCL005W-A ) or ( YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W and YGR106C and YCL005W-A )
r_0886 YMR205C or ( YGR240C and YMR205C ) YGR240C and YMR205C
r_0887 YMR205C or ( YGR240C and YMR205C ) YGR240C and YMR205C
r_2836 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2837 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2838 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2839 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2840 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2841 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2842 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_2843 YDR373W and YNL267W ( YDR373W and YNL267W ) or ( YDR373W and YNL267W and YJL100W )
r_1085 YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YMR054W and YOR332W and YPL234C and YPR036W (YPR170W-B and YBR127C and YDL185W and YOR332W and YHR026W and YEL027W and YKL080W and YLR447C and YEL051W and YPL234C and YMR054W and YGR020C and YPR036W and YHR039C-A and YGR106C and YCL005W-A) or (YBR127C and YDL185W and YOR332W and YHR026W and YEL027W and YKL080W and YLR447C and YEL051W and YPL234C and YMR054W and YGR020C and YPR036W and YHR039C-A and YGR106C and YCL005W-A)
r_1086 YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W (YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W and YPR170W-B and YGR106C and YCL005W-A) or (YBR127C and YDL185W and YEL027W and YEL051W and YGR020C and YHR026W and YHR039C-A and YKL080W and YLR447C and YOR270C and YOR332W and YPL234C and YPR036W and YGR106C and YCL005W-A)
r_0886 YMR205C or (YGR240C and YMR205C) YGR240C and YMR205C
r_0887 YMR205C or (YGR240C and YMR205C) YGR240C and YMR205C
r_2836 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2837 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2838 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2839 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2840 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2841 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2842 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
r_2843 YDR373W and YNL267W (YDR373W and YNL267W) or (YDR373W and YNL267W and YJL100W)
2 changes: 1 addition & 1 deletion model/dependencies.txt
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@@ -1,4 +1,4 @@
MATLAB 9.10.0.1602886 (R2021a)
libSBML 5.19.0
RAVEN_toolbox commit a49a911
RAVEN_toolbox commit 8aae3b8
COBRA_toolbox commit 28acb94
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